Data-driven computation of molecular reaction coordinates

Data-Driven Model Reduction and Transfer Operator Approximation

(2018) Stefan Klus et al.   JOURNAL OF NONLINEAR SCIENCE

VAMPnets for deep learning of molecular kinetics

(2018) Andreas Mardt et al.   Nature Communications

Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning

(2017) Ron Elber et al.   Entropy

Set-free Markov state model building

(2017) Marcus Weber et al.   JOURNAL OF CHEMICAL PHYSICS

Transition Manifolds of Complex Metastable Systems

(2017) Andreas Bittracher et al.   JOURNAL OF NONLINEAR SCIENCE

A Basis Set for Peptides for the Variational Approach to Conformational Kinetics

(2015) F. Vitalini et al.   Journal of Chemical Theory and Computation

Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation

(2015) Frank Noé et al.   Journal of Chemical Theory and Computation

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Exact dynamical coarse-graining without time-scale separation

(2014) Jianfeng Lu et al.   JOURNAL OF CHEMICAL PHYSICS

Recent developments in methods for identifying reaction coordinates

(2014) Wenjin Li et al.   MOLECULAR SIMULATION

Mathematical Analysis of Temperature Accelerated Dynamics

(2014) David Aristoff et al.   MULTISCALE MODELING & SIMULATION

A Computational Method to Extract Macroscopic Variables and Their Dynamics in Multiscale Systems

(2014) Gary Froyland et al.   SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

Pointwise estimates and exponential laws in metastable systems via coupling methods

(2012) Alessandra Bianchi et al.   ANNALS OF PROBABILITY

Markov state models based on milestoning

(2011) Christof Schütte et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Effective dynamics using conditional expectations

(2010) Frédéric Legoll et al.   NONLINEARITY

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Discretization of the Frobenius–Perron Operator Using a Sparse Haar Tensor Basis: The Sparse Ulam Method

(2009) Oliver Junge et al.   SIAM JOURNAL ON NUMERICAL ANALYSIS

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS

Non-linear independent component analysis with diffusion maps

(2007) Amit Singer et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS